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- PDB-6gz3: tRNA translocation by the eukaryotic 80S ribosome and the impact ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gz3 | ||||||||||||
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Title | tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1) | ||||||||||||
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![]() | RIBOSOME / translocation rabbit ribosome / 80S / eEF2 / head swivel / rotation | ||||||||||||
Function / homology | ![]() regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition ...regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / 90S preribosome / T cell proliferation involved in immune response / erythrocyte development / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / rough endoplasmic reticulum / gastrulation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA / placenta development / small-subunit processome / positive regulation of translation / protein kinase C binding / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / glucose homeostasis / ribosome binding / retina development in camera-type eye / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / postsynaptic density / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / positive regulation of apoptotic process / centrosome / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / nucleolus / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / Golgi apparatus / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
![]() | Flis, J. / Holm, M. / Rundlet, E.J. / Loerke, J. / Hilal, T. / Dabrowski, M. / Buerger, J. / Mielke, T. / Blanchard, S.C. / Spahn, C.M.T. / Budkevich, T.V. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Authors: Julia Flis / Mikael Holm / Emily J Rundlet / Justus Loerke / Tarek Hilal / Marylena Dabrowski / Jörg Bürger / Thorsten Mielke / Scott C Blanchard / Christian M T Spahn / Tatyana V Budkevich / ![]() ![]() Abstract: Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes ...Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site. | ||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 4.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0098MC ![]() 0099C ![]() 0100C ![]() 6gz4C ![]() 6gz5C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 7 types, 7 molecules A2BvBxBwB1A3A4
#1: RNA chain | Mass: 1170164.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: RNA chain | Mass: 24437.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: RNA chain | Mass: 3837.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: RNA chain | Mass: 24533.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: RNA chain | Mass: 551108.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#39: RNA chain | Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#40: RNA chain | Mass: 38385.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+Ribosomal protein ... , 72 types, 72 molecules BDBFBKBPBQBRBSBTBUBZBcBdBfBgBABCBEBIBJBLBNBOBVBWBXBYBaBbBeAA...
-40S ribosomal protein ... , 4 types, 4 molecules BMBBBGBH
#9: Protein | Mass: 13393.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#22: Protein | Mass: 24660.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#25: Protein | Mass: 26913.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#26: Protein | Mass: 20990.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 3 types, 3 molecules AZAuCt
#65: Protein | Mass: 15647.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#83: Protein | Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#86: Protein | Mass: 95056.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 3 types, 333 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GNP.gif)
#87: Chemical | ChemComp-MG / #88: Chemical | ChemComp-ZN / #89: Chemical | ChemComp-GNP / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component |
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Molecular weight | Value: 4.3 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 5 sec. / Electron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Particle selection | Num. of particles selected: 270000 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32386 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |